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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        This report was generated using MultiQC, version 1.13.dev0

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-08-19, 14:02 EDT based on data in: /restricted/projectnb/infant-microbiome/work/aodom/HIV_Exposed_Infants/fastqc_results


        General Statistics

        Showing 334/334 rows and 4/5 columns.
        Sample Name% Dups% GCRead LengthM Seqs
        X10062_S85_L001_R1_001
        86.6%
        51%
        299 bp
        0.1
        X10062_S85_L001_R2_001
        88.9%
        52%
        299 bp
        0.1
        X10064_S92_L001_R1_001
        92.3%
        51%
        301 bp
        0.1
        X10064_S92_L001_R2_001
        94.0%
        52%
        301 bp
        0.1
        X10255_S41_L001_R1_001
        90.5%
        51%
        297 bp
        0.0
        X10255_S41_L001_R2_001
        86.3%
        50%
        299 bp
        0.0
        X10401_S94_L001_R1_001
        72.2%
        51%
        288 bp
        0.1
        X10401_S94_L001_R2_001
        67.3%
        50%
        291 bp
        0.1
        X10402_S6_L001_R1_001
        94.9%
        51%
        300 bp
        0.1
        X10402_S6_L001_R2_001
        92.7%
        51%
        301 bp
        0.1
        X10590_S8_L001_R1_001
        96.4%
        51%
        300 bp
        0.1
        X10590_S8_L001_R2_001
        94.2%
        50%
        301 bp
        0.1
        X10592_S15_L001_R1_001
        95.8%
        51%
        301 bp
        0.1
        X10592_S15_L001_R2_001
        94.1%
        51%
        301 bp
        0.1
        X10724_S50_L001_R1_001
        96.0%
        51%
        301 bp
        0.1
        X10724_S50_L001_R2_001
        94.5%
        52%
        301 bp
        0.1
        X10754_S10_L001_R1_001
        94.1%
        54%
        301 bp
        0.2
        X10754_S10_L001_R2_001
        92.1%
        54%
        301 bp
        0.2
        X10892_S45_L001_R1_001
        94.9%
        53%
        301 bp
        0.2
        X10892_S45_L001_R2_001
        91.7%
        52%
        301 bp
        0.2
        X10907_S28_L001_R1_001
        94.2%
        52%
        301 bp
        0.2
        X10907_S28_L001_R2_001
        91.6%
        51%
        301 bp
        0.2
        X10973_S19_L001_R1_001
        94.2%
        52%
        301 bp
        0.1
        X10973_S19_L001_R2_001
        91.4%
        51%
        301 bp
        0.1
        X10986_S53_L001_R1_001
        92.5%
        54%
        301 bp
        0.1
        X10986_S53_L001_R2_001
        91.5%
        54%
        301 bp
        0.1
        X11041_S17_L001_R1_001
        96.4%
        52%
        301 bp
        0.1
        X11041_S17_L001_R2_001
        94.8%
        51%
        301 bp
        0.1
        X11043_S24_L001_R1_001
        93.3%
        51%
        298 bp
        0.1
        X11043_S24_L001_R2_001
        90.1%
        50%
        299 bp
        0.1
        X11120_S61_L001_R1_001
        94.3%
        52%
        301 bp
        0.2
        X11120_S61_L001_R2_001
        92.5%
        52%
        301 bp
        0.2
        X11170_S68_L001_R1_001
        96.5%
        52%
        300 bp
        0.0
        X11170_S68_L001_R2_001
        94.0%
        50%
        301 bp
        0.0
        X11220_S1_L001_R1_001
        92.1%
        52%
        301 bp
        0.1
        X11220_S1_L001_R2_001
        90.7%
        51%
        301 bp
        0.1
        X11244_S59_L001_R1_001
        95.0%
        52%
        301 bp
        0.0
        X11244_S59_L001_R2_001
        93.6%
        53%
        301 bp
        0.0
        X11269_S26_L001_R1_001
        89.6%
        53%
        294 bp
        0.0
        X11269_S26_L001_R2_001
        84.3%
        51%
        297 bp
        0.0
        X11270_S33_L001_R1_001
        94.7%
        52%
        301 bp
        0.1
        X11270_S33_L001_R2_001
        92.4%
        51%
        301 bp
        0.1
        X11373_S35_L001_R1_001
        89.5%
        52%
        298 bp
        0.0
        X11373_S35_L001_R2_001
        86.7%
        51%
        299 bp
        0.0
        X11374_S42_L001_R1_001
        95.6%
        52%
        301 bp
        0.1
        X11374_S42_L001_R2_001
        93.0%
        50%
        301 bp
        0.1
        X11376_S70_L001_R1_001
        94.3%
        52%
        301 bp
        0.2
        X11376_S70_L001_R2_001
        92.5%
        52%
        301 bp
        0.2
        X11822_S11_L001_R1_001
        90.5%
        54%
        301 bp
        0.0
        X11822_S11_L001_R2_001
        89.5%
        52%
        301 bp
        0.0
        X11916_S20_L001_R1_001
        93.1%
        53%
        301 bp
        0.1
        X11916_S20_L001_R2_001
        89.9%
        52%
        301 bp
        0.1
        X12080_S46_L001_R1_001
        93.6%
        52%
        301 bp
        0.1
        X12080_S46_L001_R2_001
        91.4%
        52%
        301 bp
        0.1
        X12115_S2_L001_R1_001
        92.8%
        52%
        301 bp
        0.1
        X12115_S2_L001_R2_001
        91.8%
        52%
        301 bp
        0.1
        X12136_S29_L001_R1_001
        92.6%
        53%
        301 bp
        0.2
        X12136_S29_L001_R2_001
        90.7%
        53%
        301 bp
        0.2
        X12185_S44_L001_R1_001
        89.5%
        52%
        299 bp
        0.0
        X12185_S44_L001_R2_001
        84.8%
        52%
        300 bp
        0.0
        X12187_S51_L001_R1_001
        94.6%
        52%
        301 bp
        0.1
        X12187_S51_L001_R2_001
        92.8%
        51%
        301 bp
        0.1
        X12327_S62_L001_R1_001
        90.0%
        52%
        301 bp
        0.1
        X12327_S62_L001_R2_001
        89.1%
        53%
        301 bp
        0.1
        X12342_S53_L001_R1_001
        91.9%
        52%
        300 bp
        0.0
        X12342_S53_L001_R2_001
        89.4%
        51%
        300 bp
        0.0
        X12344_S60_L001_R1_001
        94.4%
        52%
        301 bp
        0.0
        X12344_S60_L001_R2_001
        93.0%
        51%
        301 bp
        0.0
        X12455_S62_L001_R1_001
        85.4%
        52%
        289 bp
        0.0
        X12455_S62_L001_R2_001
        79.5%
        51%
        290 bp
        0.0
        X12456_S69_L001_R1_001
        92.7%
        52%
        295 bp
        0.1
        X12456_S69_L001_R2_001
        90.9%
        50%
        296 bp
        0.1
        X12504_S71_L001_R1_001
        93.7%
        52%
        301 bp
        0.1
        X12504_S71_L001_R2_001
        92.7%
        53%
        301 bp
        0.1
        X12838_S5_L001_R1_001
        84.8%
        52%
        301 bp
        0.1
        X12838_S5_L001_R2_001
        80.7%
        52%
        301 bp
        0.1
        X12840_S12_L001_R1_001
        93.8%
        54%
        301 bp
        0.2
        X12840_S12_L001_R2_001
        92.0%
        52%
        301 bp
        0.2
        X13074_S72_L001_R1_001
        94.4%
        52%
        301 bp
        0.2
        X13074_S72_L001_R2_001
        93.2%
        53%
        301 bp
        0.2
        X13183_S14_L001_R1_001
        92.9%
        54%
        301 bp
        0.1
        X13183_S14_L001_R2_001
        90.1%
        54%
        301 bp
        0.1
        X13184_S21_L001_R1_001
        94.4%
        53%
        301 bp
        0.2
        X13184_S21_L001_R2_001
        91.8%
        52%
        301 bp
        0.2
        X13219_S54_L001_R1_001
        92.1%
        52%
        301 bp
        0.2
        X13219_S54_L001_R2_001
        90.4%
        52%
        301 bp
        0.2
        X13281_S23_L001_R1_001
        92.8%
        53%
        301 bp
        0.1
        X13281_S23_L001_R2_001
        90.5%
        52%
        301 bp
        0.1
        X13283_S30_L001_R1_001
        92.8%
        51%
        301 bp
        0.2
        X13283_S30_L001_R2_001
        90.2%
        52%
        301 bp
        0.2
        X13354_S47_L001_R1_001
        93.6%
        53%
        301 bp
        0.1
        X13354_S47_L001_R2_001
        91.4%
        52%
        301 bp
        0.1
        X13473_S71_L001_R1_001
        92.9%
        52%
        300 bp
        0.0
        X13473_S71_L001_R2_001
        90.3%
        51%
        300 bp
        0.0
        X13474_S3_L001_R1_001
        92.7%
        52%
        301 bp
        0.1
        X13474_S3_L001_R2_001
        92.0%
        52%
        301 bp
        0.1
        X13530_S63_L001_R1_001
        93.5%
        52%
        301 bp
        0.2
        X13530_S63_L001_R2_001
        91.7%
        52%
        301 bp
        0.2
        X14194_S55_L001_R1_001
        93.5%
        51%
        301 bp
        0.2
        X14194_S55_L001_R2_001
        93.1%
        52%
        301 bp
        0.2
        X14385_S41_L001_R1_001
        94.7%
        52%
        301 bp
        0.1
        X14385_S41_L001_R2_001
        92.2%
        52%
        301 bp
        0.1
        X14387_S48_L001_R1_001
        85.5%
        53%
        301 bp
        0.0
        X14387_S48_L001_R2_001
        81.2%
        52%
        301 bp
        0.0
        X14502_S64_L001_R1_001
        94.0%
        51%
        301 bp
        0.3
        X14502_S64_L001_R2_001
        92.6%
        52%
        301 bp
        0.3
        X14800_S73_L001_R1_001
        93.6%
        51%
        301 bp
        0.2
        X14800_S73_L001_R2_001
        92.4%
        52%
        301 bp
        0.2
        X15367_S50_L001_R1_001
        86.7%
        53%
        301 bp
        0.1
        X15367_S50_L001_R2_001
        84.3%
        53%
        301 bp
        0.1
        X15368_S56_L001_R1_001
        94.1%
        51%
        301 bp
        0.1
        X15368_S56_L001_R2_001
        92.5%
        52%
        301 bp
        0.1
        X15601_S65_L001_R1_001
        87.5%
        52%
        301 bp
        0.1
        X15601_S65_L001_R2_001
        85.6%
        52%
        301 bp
        0.1
        X15925_S74_L001_R1_001
        92.3%
        51%
        301 bp
        0.1
        X15925_S74_L001_R2_001
        84.1%
        51%
        301 bp
        0.1
        X15926_S67_L001_R1_001
        89.4%
        51%
        301 bp
        0.1
        X15926_S67_L001_R2_001
        86.9%
        51%
        301 bp
        0.1
        X1754_S75_L001_R1_001
        91.4%
        53%
        300 bp
        0.1
        X1754_S75_L001_R2_001
        92.7%
        52%
        301 bp
        0.1
        X1755_S77_L001_R1_001
        89.7%
        56%
        298 bp
        0.1
        X1755_S77_L001_R2_001
        91.3%
        55%
        300 bp
        0.1
        X2214_S84_L001_R1_001
        84.6%
        53%
        294 bp
        0.1
        X2214_S84_L001_R2_001
        85.3%
        53%
        296 bp
        0.1
        X2216_S86_L001_R1_001
        91.6%
        53%
        301 bp
        0.1
        X2216_S86_L001_R2_001
        91.9%
        53%
        301 bp
        0.1
        X2429_S93_L001_R1_001
        90.7%
        54%
        298 bp
        0.1
        X2429_S93_L001_R2_001
        90.5%
        52%
        300 bp
        0.1
        X2431_S95_L001_R1_001
        91.9%
        54%
        300 bp
        0.1
        X2431_S95_L001_R2_001
        92.5%
        53%
        301 bp
        0.1
        X2561_S9_L001_R1_001
        95.6%
        56%
        299 bp
        0.1
        X2561_S9_L001_R2_001
        93.3%
        53%
        301 bp
        0.1
        X2562_S7_L001_R1_001
        96.6%
        52%
        301 bp
        0.1
        X2562_S7_L001_R2_001
        94.8%
        51%
        301 bp
        0.1
        X2697_S16_L001_R1_001
        90.4%
        51%
        289 bp
        0.0
        X2697_S16_L001_R2_001
        85.8%
        51%
        292 bp
        0.0
        X2699_S18_L001_R1_001
        95.8%
        56%
        301 bp
        0.1
        X2699_S18_L001_R2_001
        92.7%
        53%
        301 bp
        0.1
        X2927_S78_L001_R1_001
        91.3%
        53%
        300 bp
        0.1
        X2927_S78_L001_R2_001
        90.8%
        53%
        300 bp
        0.1
        X3042_S25_L001_R1_001
        90.4%
        56%
        299 bp
        0.1
        X3042_S25_L001_R2_001
        88.2%
        54%
        301 bp
        0.1
        X3043_S27_L001_R1_001
        96.1%
        52%
        301 bp
        0.1
        X3043_S27_L001_R2_001
        94.1%
        51%
        301 bp
        0.1
        X3266_S87_L001_R1_001
        90.3%
        52%
        301 bp
        0.1
        X3266_S87_L001_R2_001
        92.6%
        52%
        301 bp
        0.1
        X3306_S36_L001_R1_001
        94.9%
        52%
        299 bp
        0.1
        X3306_S36_L001_R2_001
        91.6%
        51%
        300 bp
        0.1
        X3308_S34_L001_R1_001
        85.4%
        53%
        297 bp
        0.0
        X3308_S34_L001_R2_001
        78.6%
        52%
        298 bp
        0.0
        X3646_S1_L001_R1_001
        94.2%
        52%
        300 bp
        0.1
        X3646_S1_L001_R2_001
        92.7%
        51%
        301 bp
        0.1
        X3847_S45_L001_R1_001
        96.6%
        52%
        301 bp
        0.1
        X3847_S45_L001_R2_001
        94.6%
        51%
        301 bp
        0.1
        X3848_S43_L001_R1_001
        91.8%
        51%
        299 bp
        0.0
        X3848_S43_L001_R2_001
        88.7%
        50%
        300 bp
        0.0
        X3897_S19_L001_R1_001
        88.3%
        50%
        281 bp
        0.0
        X3897_S19_L001_R2_001
        81.4%
        49%
        287 bp
        0.0
        X3928_S10_L001_R1_001
        95.5%
        51%
        301 bp
        0.1
        X3928_S10_L001_R2_001
        93.9%
        51%
        301 bp
        0.1
        X4212_S28_L001_R1_001
        93.6%
        54%
        299 bp
        0.1
        X4212_S28_L001_R2_001
        90.8%
        52%
        301 bp
        0.1
        X4247_S63_L001_R1_001
        95.0%
        53%
        300 bp
        0.1
        X4247_S63_L001_R2_001
        92.3%
        52%
        301 bp
        0.1
        X4249_S61_L001_R1_001
        90.1%
        53%
        296 bp
        0.1
        X4249_S61_L001_R2_001
        87.1%
        52%
        297 bp
        0.1
        X4335_S52_L001_R1_001
        91.6%
        52%
        300 bp
        0.0
        X4335_S52_L001_R2_001
        89.2%
        51%
        300 bp
        0.0
        X4336_S54_L001_R1_001
        96.0%
        52%
        300 bp
        0.1
        X4336_S54_L001_R2_001
        93.7%
        51%
        301 bp
        0.1
        X4632_S37_L001_R1_001
        91.6%
        52%
        295 bp
        0.1
        X4632_S37_L001_R2_001
        90.1%
        51%
        295 bp
        0.1
        X4753_S70_L001_R1_001
        89.4%
        53%
        298 bp
        0.0
        X4753_S70_L001_R2_001
        86.2%
        52%
        298 bp
        0.0
        X4755_S72_L001_R1_001
        96.1%
        52%
        301 bp
        0.1
        X4755_S72_L001_R2_001
        94.3%
        51%
        301 bp
        0.1
        X4756_S79_L001_R1_001
        86.0%
        52%
        300 bp
        0.1
        X4756_S79_L001_R2_001
        87.0%
        51%
        300 bp
        0.1
        X4927_S6_L001_R1_001
        94.8%
        52%
        301 bp
        0.2
        X4927_S6_L001_R2_001
        91.3%
        53%
        301 bp
        0.2
        X4928_S4_L001_R1_001
        87.3%
        54%
        301 bp
        0.1
        X4928_S4_L001_R2_001
        86.0%
        54%
        301 bp
        0.1
        X5031_S46_L001_R1_001
        86.3%
        52%
        296 bp
        0.0
        X5031_S46_L001_R2_001
        80.5%
        50%
        298 bp
        0.0
        X5035_S11_L001_R1_001
        95.2%
        52%
        301 bp
        0.0
        X5035_S11_L001_R2_001
        93.5%
        51%
        301 bp
        0.0
        X5036_S22_L001_R1_001
        94.0%
        53%
        301 bp
        0.2
        X5036_S22_L001_R2_001
        90.8%
        52%
        301 bp
        0.2
        X5037_S24_L001_R1_001
        94.0%
        54%
        301 bp
        0.2
        X5037_S24_L001_R2_001
        90.7%
        53%
        301 bp
        0.2
        X5042_S88_L001_R1_001
        90.6%
        52%
        301 bp
        0.1
        X5042_S88_L001_R2_001
        92.5%
        52%
        301 bp
        0.1
        X5116_S2_L001_R1_001
        95.1%
        51%
        301 bp
        0.1
        X5116_S2_L001_R2_001
        94.0%
        52%
        301 bp
        0.1
        X5186_S29_L001_R1_001
        89.4%
        52%
        299 bp
        0.0
        X5186_S29_L001_R2_001
        85.2%
        50%
        300 bp
        0.0
        X5218_S13_L001_R1_001
        91.7%
        54%
        301 bp
        0.2
        X5218_S13_L001_R2_001
        88.8%
        54%
        301 bp
        0.2
        X5220_S15_L001_R1_001
        95.2%
        52%
        301 bp
        0.2
        X5220_S15_L001_R2_001
        91.8%
        51%
        301 bp
        0.2
        X5382_S33_L001_R1_001
        95.1%
        52%
        301 bp
        0.2
        X5382_S33_L001_R2_001
        93.1%
        53%
        301 bp
        0.2
        X5383_S31_L001_R1_001
        85.5%
        52%
        301 bp
        0.1
        X5383_S31_L001_R2_001
        81.9%
        52%
        301 bp
        0.1
        X5449_S20_L001_R1_001
        93.6%
        48%
        300 bp
        0.0
        X5449_S20_L001_R2_001
        90.6%
        49%
        301 bp
        0.0
        X5650_S64_L001_R1_001
        92.9%
        53%
        300 bp
        0.0
        X5650_S64_L001_R2_001
        90.3%
        52%
        301 bp
        0.0
        X5659_S35_L001_R1_001
        80.0%
        53%
        301 bp
        0.1
        X5659_S35_L001_R2_001
        81.0%
        52%
        301 bp
        0.1
        X5660_S37_L001_R1_001
        94.2%
        52%
        301 bp
        0.2
        X5660_S37_L001_R2_001
        91.2%
        52%
        301 bp
        0.2
        X5806_S55_L001_R1_001
        95.3%
        52%
        300 bp
        0.1
        X5806_S55_L001_R2_001
        93.7%
        51%
        301 bp
        0.1
        X6202_S80_L001_R1_001
        85.8%
        53%
        299 bp
        0.1
        X6202_S80_L001_R2_001
        84.9%
        52%
        300 bp
        0.1
        X6214_S73_L001_R1_001
        94.1%
        52%
        301 bp
        0.1
        X6214_S73_L001_R2_001
        91.5%
        51%
        301 bp
        0.1
        X6280_S25_L001_R1_001
        94.7%
        52%
        301 bp
        0.2
        X6280_S25_L001_R2_001
        93.1%
        52%
        301 bp
        0.2
        X6354_S89_L001_R1_001
        92.0%
        52%
        301 bp
        0.1
        X6354_S89_L001_R2_001
        94.2%
        52%
        301 bp
        0.1
        X6474_S7_L001_R1_001
        91.5%
        56%
        301 bp
        0.1
        X6474_S7_L001_R2_001
        88.5%
        54%
        301 bp
        0.1
        X6534_S16_L001_R1_001
        96.9%
        54%
        301 bp
        1.9
        X6534_S16_L001_R2_001
        94.3%
        52%
        301 bp
        1.9
        X6541_S38_L001_R1_001
        94.3%
        51%
        299 bp
        0.0
        X6541_S38_L001_R2_001
        92.7%
        51%
        300 bp
        0.0
        X6644_S3_L001_R1_001
        94.6%
        51%
        301 bp
        0.0
        X6644_S3_L001_R2_001
        92.8%
        51%
        301 bp
        0.0
        X6822_S12_L001_R1_001
        94.5%
        52%
        300 bp
        0.1
        X6822_S12_L001_R2_001
        93.3%
        51%
        301 bp
        0.1
        X6863_S32_L001_R1_001
        86.9%
        52%
        301 bp
        0.1
        X6863_S32_L001_R2_001
        83.5%
        53%
        301 bp
        0.1
        X6864_S34_L001_R1_001
        93.3%
        52%
        301 bp
        0.1
        X6864_S34_L001_R2_001
        89.9%
        52%
        301 bp
        0.1
        X6870_S47_L001_R1_001
        93.7%
        53%
        300 bp
        0.0
        X6870_S47_L001_R2_001
        91.7%
        52%
        301 bp
        0.0
        X7031_S42_L001_R1_001
        95.0%
        55%
        301 bp
        0.2
        X7031_S42_L001_R2_001
        91.4%
        54%
        301 bp
        0.2
        X7090_S38_L001_R1_001
        95.0%
        51%
        301 bp
        0.1
        X7090_S38_L001_R2_001
        93.1%
        52%
        301 bp
        0.1
        X7223_S21_L001_R1_001
        93.4%
        51%
        300 bp
        0.1
        X7223_S21_L001_R2_001
        91.2%
        50%
        300 bp
        0.1
        X7272_S65_L001_R1_001
        90.6%
        52%
        299 bp
        0.0
        X7272_S65_L001_R2_001
        86.7%
        52%
        300 bp
        0.0
        X7274_S90_L001_R1_001
        89.9%
        52%
        300 bp
        0.1
        X7274_S90_L001_R2_001
        91.0%
        52%
        300 bp
        0.1
        X7288_S56_L001_R1_001
        93.7%
        52%
        300 bp
        0.0
        X7288_S56_L001_R2_001
        91.3%
        51%
        301 bp
        0.0
        X7426_S30_L001_R1_001
        96.3%
        52%
        299 bp
        0.2
        X7426_S30_L001_R2_001
        93.3%
        51%
        301 bp
        0.2
        X7448_S81_L001_R1_001
        93.8%
        52%
        301 bp
        0.1
        X7448_S81_L001_R2_001
        93.9%
        51%
        301 bp
        0.1
        X7695_S39_L001_R1_001
        95.2%
        52%
        300 bp
        0.0
        X7695_S39_L001_R2_001
        93.0%
        50%
        301 bp
        0.0
        X7746_S4_L001_R1_001
        94.2%
        53%
        301 bp
        0.0
        X7746_S4_L001_R2_001
        92.3%
        52%
        301 bp
        0.0
        X7958_S13_L001_R1_001
        95.0%
        52%
        300 bp
        0.1
        X7958_S13_L001_R2_001
        93.3%
        51%
        301 bp
        0.1
        X8066_S74_L001_R1_001
        94.9%
        52%
        301 bp
        0.0
        X8066_S74_L001_R2_001
        89.7%
        50%
        301 bp
        0.0
        X8180_S43_L001_R1_001
        94.5%
        55%
        301 bp
        0.2
        X8180_S43_L001_R2_001
        91.9%
        54%
        301 bp
        0.2
        X8261_S57_L001_R1_001
        93.7%
        52%
        301 bp
        0.2
        X8261_S57_L001_R2_001
        92.2%
        52%
        301 bp
        0.2
        X8262_S59_L001_R1_001
        91.9%
        52%
        301 bp
        0.1
        X8262_S59_L001_R2_001
        90.3%
        51%
        301 bp
        0.1
        X8268_S26_L001_R1_001
        97.7%
        53%
        301 bp
        3.3
        X8268_S26_L001_R2_001
        95.5%
        51%
        301 bp
        3.3
        X8285_S49_L001_R1_001
        88.5%
        54%
        301 bp
        0.2
        X8285_S49_L001_R2_001
        86.7%
        53%
        301 bp
        0.2
        X8287_S51_L001_R1_001
        94.3%
        53%
        301 bp
        0.2
        X8287_S51_L001_R2_001
        92.3%
        53%
        301 bp
        0.2
        X8288_S8_L001_R1_001
        92.6%
        53%
        301 bp
        0.2
        X8288_S8_L001_R2_001
        88.9%
        53%
        301 bp
        0.2
        X8312_S17_L001_R1_001
        93.4%
        52%
        301 bp
        0.1
        X8312_S17_L001_R2_001
        90.2%
        52%
        301 bp
        0.1
        X8332_S48_L001_R1_001
        93.0%
        53%
        300 bp
        0.1
        X8332_S48_L001_R2_001
        89.7%
        52%
        300 bp
        0.1
        X8500_S22_L001_R1_001
        95.8%
        51%
        301 bp
        0.1
        X8500_S22_L001_R2_001
        93.9%
        50%
        301 bp
        0.1
        X8550_S66_L001_R1_001
        98.3%
        52%
        301 bp
        0.3
        X8550_S66_L001_R2_001
        96.2%
        51%
        301 bp
        0.3
        X8607_S66_L001_R1_001
        93.9%
        52%
        301 bp
        0.2
        X8607_S66_L001_R2_001
        91.5%
        52%
        301 bp
        0.2
        X8608_S68_L001_R1_001
        93.9%
        53%
        301 bp
        0.1
        X8608_S68_L001_R2_001
        89.8%
        53%
        301 bp
        0.1
        X8686_S36_L001_R1_001
        94.0%
        51%
        301 bp
        0.2
        X8686_S36_L001_R2_001
        91.4%
        52%
        301 bp
        0.2
        X8688_S39_L001_R1_001
        93.9%
        51%
        301 bp
        0.1
        X8688_S39_L001_R2_001
        91.1%
        52%
        301 bp
        0.1
        X8726_S31_L001_R1_001
        93.2%
        52%
        299 bp
        0.1
        X8726_S31_L001_R2_001
        90.7%
        50%
        300 bp
        0.1
        X8736_S91_L001_R1_001
        88.9%
        51%
        301 bp
        0.1
        X8736_S91_L001_R2_001
        92.1%
        52%
        301 bp
        0.1
        X8742_S57_L001_R1_001
        95.6%
        52%
        300 bp
        0.1
        X8742_S57_L001_R2_001
        93.7%
        51%
        301 bp
        0.1
        X8789_S82_L001_R1_001
        91.4%
        52%
        300 bp
        0.1
        X8789_S82_L001_R2_001
        92.3%
        51%
        300 bp
        0.1
        X9000_S40_L001_R1_001
        95.6%
        52%
        301 bp
        0.1
        X9000_S40_L001_R2_001
        93.9%
        51%
        301 bp
        0.1
        X9080_S5_L001_R1_001
        96.0%
        52%
        301 bp
        0.1
        X9080_S5_L001_R2_001
        94.8%
        52%
        301 bp
        0.1
        X9376_S75_L001_R1_001
        94.9%
        51%
        301 bp
        0.0
        X9376_S75_L001_R2_001
        92.5%
        51%
        301 bp
        0.0
        X9384_S52_L001_R1_001
        92.8%
        54%
        301 bp
        0.2
        X9384_S52_L001_R2_001
        91.2%
        53%
        301 bp
        0.2
        X9424_S60_L001_R1_001
        93.7%
        53%
        301 bp
        0.1
        X9424_S60_L001_R2_001
        91.5%
        52%
        301 bp
        0.1
        X9518_S9_L001_R1_001
        93.7%
        52%
        301 bp
        0.2
        X9518_S9_L001_R2_001
        91.6%
        52%
        301 bp
        0.2
        X9555_S23_L001_R1_001
        91.0%
        52%
        296 bp
        0.0
        X9555_S23_L001_R2_001
        87.0%
        51%
        298 bp
        0.0
        X9572_S14_L001_R1_001
        96.4%
        51%
        301 bp
        0.1
        X9572_S14_L001_R2_001
        94.9%
        51%
        301 bp
        0.1
        X9603_S49_L001_R1_001
        93.2%
        52%
        300 bp
        0.0
        X9603_S49_L001_R2_001
        91.6%
        51%
        301 bp
        0.0
        X9632_S18_L001_R1_001
        93.7%
        53%
        301 bp
        0.2
        X9632_S18_L001_R2_001
        89.8%
        52%
        301 bp
        0.2
        X9684_S27_L001_R1_001
        92.5%
        51%
        301 bp
        0.1
        X9684_S27_L001_R2_001
        90.4%
        51%
        301 bp
        0.1
        X9708_S69_L001_R1_001
        94.8%
        53%
        301 bp
        0.2
        X9708_S69_L001_R2_001
        92.1%
        53%
        301 bp
        0.2
        X9714_S32_L001_R1_001
        94.6%
        52%
        301 bp
        0.0
        X9714_S32_L001_R2_001
        92.0%
        51%
        301 bp
        0.0
        X9922_S44_L001_R1_001
        92.6%
        54%
        301 bp
        0.1
        X9922_S44_L001_R2_001
        88.8%
        54%
        301 bp
        0.1
        X9956_S58_L001_R1_001
        93.7%
        54%
        300 bp
        0.0
        X9956_S58_L001_R2_001
        91.1%
        52%
        301 bp
        0.0
        X9983_S76_L001_R1_001
        91.4%
        52%
        300 bp
        0.2
        X9983_S76_L001_R2_001
        92.3%
        52%
        300 bp
        0.2
        X9984_S83_L001_R1_001
        92.3%
        52%
        301 bp
        0.1
        X9984_S83_L001_R2_001
        94.1%
        52%
        301 bp
        0.1

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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